dbSNP rs838883: SCARB1:c.*1294A>G (chr12-124777293-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005505.5(SCARB1):c.*1294A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,224 control chromosomes in the GnomAD database, including 65,323 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.93 ( 65320 hom., cov: 32)

Exomes 𝑓: 0.75 ( 3 hom. )

Consequence

SCARB1
NM_005505.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.196

Publications

6 publications found

Variant links:

Genes affected

SCARB1 (HGNC:1664): (scavenger receptor class B member 1) The protein encoded by this gene is a plasma membrane receptor for high density lipoprotein cholesterol (HDL). The encoded protein mediates cholesterol transfer to and from HDL. In addition, this protein is a receptor for hepatitis C virus glycoprotein E2 and facilitates cell entry by the virus, SARS-CoV2. [provided by RefSeq, Oct 2021]

SCARB1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005505.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SCARB1	NM_005505.5	MANE Select	c.*1294A>G	3_prime_UTR	Exon 13 of 13	NP_005496.4
SCARB1	NM_001367981.1		c.*1286A>G	3_prime_UTR	Exon 12 of 12	NP_001354910.1	Q8WTV0-1
SCARB1	NM_001367983.1		c.*1294A>G	3_prime_UTR	Exon 13 of 13	NP_001354912.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SCARB1	ENST00000261693.11	TSL:1 MANE Select	c.*1294A>G	3_prime_UTR	Exon 13 of 13	ENSP00000261693.6	Q8WTV0-2
SCARB1	ENST00000339570.9	TSL:5	c.*1174A>G	3_prime_UTR	Exon 12 of 12	ENSP00000343795.4	Q8WTV0-5
SCARB1	ENST00000680596.1		c.*1174A>G	3_prime_UTR	Exon 12 of 12	ENSP00000505605.1	A0A7P0T9I2

Frequencies

GnomAD3 genomes

AF:

0.926

AC:

140829

AN:

152094

Hom.:

65260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.934

Gnomad AMI

AF:

0.968

Gnomad AMR

AF:

0.953

Gnomad ASJ

AF:

0.950

Gnomad EAS

AF:

0.996

Gnomad SAS

AF:

0.855

Gnomad FIN

AF:

0.828

Gnomad MID

AF:

0.943

Gnomad NFE

AF:

0.928

Gnomad OTH

AF:

0.938

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.926

AC:

140949

AN:

152212

Hom.:

65320

Cov.:

AF XY:

0.922

AC XY:

68559

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.934

AC:

38799

AN:

41554

American (AMR)

AF:

0.953

AC:

14556

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.950

AC:

3300

AN:

3472

East Asian (EAS)

AF:

0.996

AC:

5155

AN:

5178

South Asian (SAS)

AF:

0.855

AC:

4131

AN:

4830

European-Finnish (FIN)

AF:

0.828

AC:

8733

AN:

10550

Middle Eastern (MID)

AF:

0.942

AC:

277

AN:

294

European-Non Finnish (NFE)

AF:

0.928

AC:

63132

AN:

68030

Other (OTH)

AF:

0.939

AC:

1985

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

530

1059

1589

2118

2648

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

908

1816

2724

3632

4540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.933

Hom.:

97418

Bravo

AF:

0.939

Asia WGS

AF:

0.920

AC:

3200

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

(source)

DANN

Benign

0.36

PhyloP100

-0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over